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As the EGA is co-managed by the EMBL-EBI and CRG, files could be located in the UK and/or Spain, as indicated by their respective flags.

Alternatively, files could be located in one of the international Federated EGA nodes, as indicated next to the node's flag.
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STimage: Robust and interpretable prediction of gene markers and cell types from spatial transcriptomics data

This dataset comprises raw sequencing data (FASTQ files) derived from 13 Formalin-Fixed Paraffin-Embedded (FFPE) melanoma tissue samples profiled using the 10x Genomics Visium platform. These spatially resolved transcriptomic profiles serve as the primary dataset for the STimage study, enabling the development and benchmarking of deep learning models that predict gene expression directly from H&E histology images.

Request Access

DUO:0000021
version: 2021-02-23

ethics approval required

This data use modifier indicates that the requestor must provide documentation of local IRB/ERB approval.

DUO:0000042
version: 2021-02-23

general research use

This data use permission indicates that use is allowed for general research use for any research purpose.

STimage Data Access Policy

Access to STimage datasets is granted to researchers for research only purposes. Applicants must agree to the following conditions: Intended Use: Data must be used solely for biomedical research purposes as outlined in the approved data access application. Commercial use is not permitted. Researcher Status: Applicants must be affiliated with a recognized research institution or university. Data Protection: The applicant agrees to maintain the confidentiality of the data. No attempt to identify individual participants or link the data to other sources to re-identify individuals is permitted. Sharing: The data must not be redistributed or shared with third parties not listed in the approved application. Acknowledgement: Any publications resulting from the use of this data must acknowledge the STimage project and cite the relevant primary publications. Application Process: To apply for access, please submit a Data Access Request (DAR) via the EGA account. The application should include a brief outline of the proposed research and the specific datasets requested. The STimage DAC endeavors to review all applications within 5 working days.

Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.

Study ID Study Title Study Type
EGAS50000001503 Transcriptome Sequencing

This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.

ID File Type Size Quality Report
Located in
i
EGAF50000515834 fastq.gz 338.3 MB
EGAF50000515835 fastq.gz 437.2 MB
EGAF50000515836 fastq.gz 1.2 GB
EGAF50000515837 fastq.gz 1.6 GB
EGAF50000515838 fastq.gz 339.0 MB
EGAF50000515839 fastq.gz 438.6 MB
EGAF50000515840 fastq.gz 1.2 GB
EGAF50000515841 fastq.gz 1.6 GB
EGAF50000515842 fastq.gz 344.6 MB
EGAF50000515843 fastq.gz 443.4 MB
EGAF50000515844 fastq.gz 1.3 GB
EGAF50000515845 fastq.gz 1.8 GB
EGAF50000515846 fastq.gz 343.2 MB
EGAF50000515847 fastq.gz 445.9 MB
EGAF50000515848 fastq.gz 1.3 GB
EGAF50000515849 fastq.gz 1.8 GB
EGAF50000515850 fastq.gz 258.0 MB
EGAF50000515851 fastq.gz 329.7 MB
EGAF50000515852 fastq.gz 923.7 MB
EGAF50000515853 fastq.gz 1.3 GB
EGAF50000515854 fastq.gz 267.4 MB
EGAF50000515855 fastq.gz 339.5 MB
EGAF50000515856 fastq.gz 937.3 MB
EGAF50000515857 fastq.gz 1.3 GB
EGAF50000515858 fastq.gz 435.6 MB
EGAF50000515859 fastq.gz 502.9 MB
EGAF50000515860 fastq.gz 1.6 GB
EGAF50000515861 fastq.gz 2.2 GB
EGAF50000515862 fastq.gz 449.5 MB
EGAF50000515863 fastq.gz 517.2 MB
EGAF50000515864 fastq.gz 1.6 GB
EGAF50000515865 fastq.gz 2.3 GB
EGAF50000515866 fastq.gz 360.8 MB
EGAF50000515867 fastq.gz 401.6 MB
EGAF50000515868 fastq.gz 1.2 GB
EGAF50000515869 fastq.gz 1.6 GB
EGAF50000515870 fastq.gz 367.5 MB
EGAF50000515871 fastq.gz 413.3 MB
EGAF50000515872 fastq.gz 1.2 GB
EGAF50000515873 fastq.gz 1.7 GB
40 Files (37.7 GB)